Sentence 2 needs some repair: "It has not done anything yet." "Do" is a transitive verb, remember. "It has not been done yet." This is a passive sentence. "It" receives the action, so at this point, the action is still not received or completed. "It has not done anything yet." This is an active sentence. "It" is expected to do something... but no luck so far.

When we use the present perfect ( heve/has + past participle), there is a connection with now. the action in the past has a result now: He told me his name, but "I've forgotten". ( I can't remember it now.) The 1st sentence doesn't exist! we have present perfect continuous which is built in this way: Have/Has + been + -ing form

1) IT HAS NOT BEEN DONE YET = Something has never been done (it might still be done, sometime in the future). EX: A person has not yet walked on Mars. It has not been done, yet.............................. 2) (makes no sense) but you might rephrase it with different meanings ...................(2a: It has not done anything yet = It has had no effect, yet) .... (2b: It is not done yet = It (ex: a cake) is not yet finished... maybe it is baking and it will be fully baked 10 minutes from now, but it is not done yet)